Mean new microRNA data analysis method gives sharper results
June 16, 2009Our understanding of the importance of microRNAs in regulating gene expression is expanding, and with it our requirement for robust methods to measure their expression levels. Now a new method published in BioMed Central's open access journal Genome Biology helps researchers to better understand the delicate interplay between differences in microRNA expression levels and their target genes.
Following their highly cited method for the analysis of reverse transcription quantitative PCR (RT-qPCR) expression data for mRNA transcripts, published in Genome Biology in 2007, Jo Vandesompele of the Center for Medical Genetics, Ghent University Hospital, Belgium and colleagues have created an innovative, straightforward and universally applicable method for quantitative RT-PCR data normalization for microRNAs. The researchers also provide a workflow for proper data normalization of both large scale (whole miRNome) and small-scale microRNA profiling experiments in their paper.
Vandesompele's team profiled 430 microRNAs along with 18 small RNA controls for a number of independent tissue sample sets. They assessed the use of the mean expression value of all expressed microRNAs in a given sample as a normalization factor for microRNA real-time quantitative PCR data, and then compared this method with the currently adopted approach of relying on one or two small RNA controls.
The mean expression value outperforms the current normalization strategy by better reducing technical variation and more accurately appreciating biological changes. Furthermore, normalization using microRNAs that resemble the mean expression value is platform independent and closely mimics normalization using the mean expression value.
"The mean expression value of all expressed microRNAs performs better than one based on only those microRNAs that are expressed in all samples," says Vandesompele. "This suggests a more accurate representation of input RNA fluctuations when all microRNAs are considered."
"Changes in microRNA expression are often very subtle but biologically relevant," says Pieter Mestdagh, working on the method in Vandesompele's lab. "Because microRNAs regulate genes acting in different pathways, deregulated microRNA expression can trigger a cascade of events that alter the biology of the cell. As a consequence, a proper normalization strategy that enables the detection of small changes is of utmost importance, especially when dealing with heterogeneous patient samples."
Reverse transcription quantitative PCR (RT-qPCR) has become the method of choice for measuring gene expression levels in terms of accuracy and specificity, both for coding and non-coding RNAs. However, result accuracy is largely dependent on effective data normalization.
-
MicroRNAs can be tumor suppressors
Apr 25, 2007 |
not rated yet |
0
-
Blind mice shed light on human sight loss
Nov 22, 2007 |
not rated yet |
0
-
Putting microRNAs on the stem cell map
Aug 07, 2008 |
not rated yet |
0
-
Scientists Explore Function of 'Junk DNA'
Nov 13, 2006 |
not rated yet |
0
-
Expression patterns of microRNAs appear altered in colon cancer, and associated with poor outcomes
Jan 29, 2008 |
not rated yet |
0
-
Engineers build first sub-10-nm carbon nanotube transistor
Feb 01, 2012 |
4.9 / 5 (33) |
30
-
Something old, something new: Evolution and the structural divergence of duplicate genes
Jan 31, 2012 |
4.6 / 5 (7) |
1
-
The hidden nanoworld of ice crystals: Revealing the dynamic behavior of quasi-liquid layers
Jan 30, 2012 |
5 / 5 (4) |
1
-
Stock market network reveals investor clustering
Jan 27, 2012 |
3.9 / 5 (23) |
8
-
Of microchemistry and molecules: Electronic microfluidic device synthesizes biocompatible probes
Jan 26, 2012 |
5 / 5 (2) |
0
-
Classical and Quantum Mechanics via Lie algebras
Apr 15, 2011
- More from Physics Forums - Independent Research
More news stories
Overeating may double risk of memory loss
New research suggests that consuming between 2,100 and 6,000 calories per day may double the risk of memory loss, or mild cognitive impairment (MCI), among people age 70 and older. The study was released today and will be ...
Medicine & Health / Neuroscience
3 hours ago |
5 / 5 (2) |
0
|
Starve a virus, feed a cure? Findings show how some cells protect themselves against HIV
A protein that protects some of our immune cells from the most common and virulent form of HIV works by starving the virus of the molecular building blocks that it needs to replicate, according to research published online ...
6 hours ago |
5 / 5 (1) |
0
|
Declining health-care productivity in England: Who says so?
Reports that the National Health Service in England has been declining in productivity in the last decade appear to have been accepted as fact. However, a Viewpoint published Online First by The Lancet disputes this. The Vi ...
1 hour ago |
not rated yet |
0
Injured boomers beware: Know when to see doctor
(AP) -- It happened to nurse Jane Byron years after an in-line skating fall, business owner Haralee Weintraub while doing "men's" push-ups, and avid cyclist Gene Wilberg while lifting a heavy box.
8 hours ago |
5 / 5 (1) |
0
FDA-approved drug rapidly clears amyloid from the brain, reverses Alzheimer's symptoms in mice
Neuroscientists at Case Western Reserve University School of Medicine have made a dramatic breakthrough in their efforts to find a cure for Alzheimer's disease. The researchers' findings, published in the journal Science, show t ...
Medicine & Health / Neuroscience
Feb 09, 2012 |
4.9 / 5 (58) |
17
|
Scientists discover molecular secrets of 2,000-year-old Chinese herbal remedy
For roughly two thousand years, Chinese herbalists have treated Malaria using a root extract, commonly known as Chang Shan, from a type of hydrangea that grows in Tibet and Nepal. More recent studies suggest that halofuginone, ...
New method to examine batteries -- MRI from the inside
There is an ever-increasing need for advanced batteries for portable electronics, such as phones, cameras, and music players, but also to power electric vehicles and to facilitate the distribution and storage of energy derived ...
A mitosis mystery solved: How chromosomes align perfectly in a dividing cell
Although the process of mitotic cell division has been studied intensely for more than 50 years, Whitehead Institute researchers have only now solved the mystery of how cells correctly align their chromosomes during symmetric ...
Lab study raises questions over nano-particle impact
Tests involving chickens have raised questions about the impact on health from engineered nano-particles, the ultra-fine grains commonly used in drugs and processed foods, scientists said on Sunday.
Google might launch Drive for cloud storage soon
(PhysOrg.com) -- Google's next big move, according to the Wall Street Journal, is a cloud storage service called Drive. Hardly first to the plate, Google is simply catching up to introducing its cloud reposi ...
Researchers find extensive RNA editing in human transcriptome
In a new study published online in Nature Biotechnology, researchers from BGI, the world's largest genomics organization, reported the evidence of extensive RNA editing in a human cell line by analysis of RNA-seq data, demons ...